I had the same problem, too. Since this update seemed to have applied OK (there were no errors until it tried to restart the pedal, then couldn't locate it again), I followed the procedures in Nick's post above, restored the Factory Presets and System Settings, and everything worked as expected. This only happened on one of the Factors, though. I can't remember which one, but I think it was the MF. The others completed the entire process on their own and all were operating as expected afterwards.
Obviously, backing up your presets is important, too. There were some known issues restoring V2 presets, since that didn't support preset naming. Even then, several of the algorithms changed the range of available parameter values, which necessitated changes to earlier presets even when they were written out on paper and manually restored. In my opinion, the changes have really improved the usability and sound quality, so the growing pains have definitely been worth the effort (and occassional frustrations).